[2022-05-27 09:39:24.482] [jointLog] [info] setting maxHashResizeThreads to 6
[2022-05-27 09:39:24.482] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2022-05-27 09:39:24.482] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2022-05-27 09:39:24.482] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
[2022-05-27 09:39:24.482] [jointLog] [info] parsing read library format
[2022-05-27 09:39:24.482] [jointLog] [info] There is 1 library.
[2022-05-27 09:39:24.482] [jointLog] [info] Loading pufferfish index
[2022-05-27 09:39:24.482] [jointLog] [info] Loading dense pufferfish index.
[2022-05-27 09:39:24.545] [jointLog] [info] done
[2022-05-27 09:39:24.566] [jointLog] [info] Index contained 34752 targets
[2022-05-27 09:39:24.574] [jointLog] [info] Number of decoys : 0
[2022-05-27 09:39:24.918] [jointLog] [info] Automatically detected most likely library type as ISR

[2022-05-27 09:39:27.264] [jointLog] [info] Thread saw mini-batch with a maximum of 1.30% zero probability fragments
[2022-05-27 09:39:27.281] [jointLog] [info] Thread saw mini-batch with a maximum of 1.20% zero probability fragments
[2022-05-27 09:39:27.286] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments
[2022-05-27 09:39:27.323] [jointLog] [info] Thread saw mini-batch with a maximum of 1.32% zero probability fragments
[2022-05-27 09:39:27.370] [jointLog] [info] Thread saw mini-batch with a maximum of 1.16% zero probability fragments
[2022-05-27 09:39:27.389] [jointLog] [info] Thread saw mini-batch with a maximum of 1.14% zero probability fragments
[2022-05-27 09:39:27.469] [jointLog] [info] Computed 27479 rich equivalence classes for further processing
[2022-05-27 09:39:27.469] [jointLog] [info] Counted 446837 total reads in the equivalence classes 
[2022-05-27 09:39:27.473] [jointLog] [info] Number of mappings discarded because of alignment score : 70855
[2022-05-27 09:39:27.473] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 11346
[2022-05-27 09:39:27.473] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2022-05-27 09:39:27.473] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 14621
[2022-05-27 09:39:27.476] [jointLog] [warning] Only 446837 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2022-05-27 09:39:27.476] [jointLog] [info] Mapping rate = 89.3674%

[2022-05-27 09:39:27.476] [jointLog] [info] finished quantifyLibrary()
[2022-05-27 09:39:27.476] [jointLog] [info] Starting optimizer
[2022-05-27 09:39:27.489] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2022-05-27 09:39:27.492] [jointLog] [info] iteration = 0 | max rel diff. = 1163.97
[2022-05-27 09:39:27.470] [fileLog] [info] 
At end of round 0
==================
Observed 500000 total fragments (500000 in most recent round)

[2022-05-27 09:39:27.655] [jointLog] [info] iteration = 100 | max rel diff. = 0.232063
[2022-05-27 09:39:27.806] [jointLog] [info] iteration = 200 | max rel diff. = 0.297536
[2022-05-27 09:39:27.922] [jointLog] [info] iteration = 277 | max rel diff. = 0.00595793
[2022-05-27 09:39:27.923] [jointLog] [info] Finished optimizer
[2022-05-27 09:39:27.923] [jointLog] [info] writing output